Using OEM12C my agents wern't deploying from the OEM console. The agent home was getting created during the "agent manual deploy" option from the console. So I run this to install/start the agent on my target maching.
./agentDeploy.sh AGENT_BASE_DIR=/opt/oem12c_agentHome OMS_HOST=192.168.1.105 INVENTORY_LOCATION=/opt/oracle/app/oraInventory AGENT_REGISTRATION_PASSWORD=welcome1 EM_UPLOAD_PORT=7788